A very easy mission although possibly by design oversight. If you secure all Stations before completing main objectives, you should be fine.

Part 1 - Unlock Gate from Sector 1 to Sector 2

All Discoveries in Sectors 1 and 2 can be acquired without fighting enemy forces. The last Discovery is in Sector 3.

Two Yellow Violators will enter Sector 1 and start warping in reinforcements. Grab one there and maybe pull a Wasp to board the other as a spare. Warp one Violator to Sector 2 and start gating in reinforcements.

Possibly because neither Violator was destroyed in our playthrough (one under our control, one abandoned), there were no further attacks on Sector 1 while we cleared Sectors 2 and later Sector 3.

After this initial attack force is clear you can recycle pretty much all your ships in this Sector except for your mission-critical flagships (Ulysses I and Olympus). This lets you maximize your units securing Sector 2.

Sending a Violator over to Sector 2 is very helpful for the additional reason that their weapons are strong against Bases and have enough range to engage a Station one at a time if positioned properly. You can therefore destroy Detector stations and sneak in Wasps to steal the rest of the positions.

An alternate start in Sector 2 is to use Wasps to capture Stations and trilobites.

Wasps can Board in this Mission. Therefore there is a very real possibility of taking over the whole of Sector 2 before unlocking the gate.

Note that since Wasps can Cloak, if the Boarding action takes too long, Wasps will also Cloak during the Boarding action and stay cloaked after.

Look for a clump of Stations with no defenders and take them over with your Wasps.

If there is a Detector Station and you cannot approach Cloaked, use Wasp EMP to disable Turrets or Artillery or Interdiction before boarding.

Hang your Medusas back cloaked to counter any reinforcements from the Support Hangar in this Sector.

Remember that since a Boarding action also disables the ship or station being boarded, so you only have to rush them and start the Boarding action.

Often the Boarding action will not initiate but the target will still be neutralized. Not sure if it is just a GUI problem with the red lines and Boarding countdown not showing.

If you have enough Wasps you can sneak up on and neutralize a clump of Stations very quickly although the Boarding actions will take a while to complete.

Once you have secured a Station, reinforcements will continue to stream in to retake them. Let them come instead of destroying the Support Hangar because this is your chance to steal Trilobites. Get at least 4 (and drop all your Rovers) and also maybe keep a few inactive to be boarded later if you lose some.

Using the forces you amass, secure all Stations before unlocking the gate between Sector 1 and Sector 2.

The optional objective to board inactive ships should definitely all be done before unlocking the gate because each ship boarded adds to your Replicant total.

Two are cloaked but you can target them because of the mission-objective marker. After you have boarded at least 1 of these mission-marked ships, all markers disappear and you might not be able to find them again. Therefore use two Wasps to simultaneously board both.

When you unlock the gate, a bunch of Scythe units will come from Sector 3. Use Wasps to grab their XL ships. You may want to take one Hydra (which is good against all unit sizes and can transform into a self-healing Remora) and a Zaratan (which has very long range on its attack and therefore good for sniping enemy Stations). Dump your Medusas to do this.

Do NOT dump your Wasps! They are 1 Replicant each only and combined with their Cloaking ability are superbly useful.

Part 2 - Destroy Enemy Hangars

Leave one Support Hangar for last since they are the least dangerous and you do not want to rush to the end of this Mission -- again, our doctrine is to secure as much of a Sector as possible before advancing the story.

Capital Hangar guarded by Hydra and one Triton (that has a medium-range area EMP blast):

The conservative way is to try to lure these extra guards away or snipe at them until the extra guards are gone. Steal a Zaratan for this, dumping your Dreadnought(s) if you have to.

The faster and more exciting alternative is to rush if you have enough Wasps.

Start by sneaking Wasps into the area (their EMP range is very short). You basically need enough Wasps to disable everything that can kill them too quickly.

Being your approach with the rest of the fleet. Before the Triton can EMP your fleet, use your Wasps to EMP the Triton as well as other key units or Stations. To disable the rest, begin Boarding actions on them with your Wasps. With 4 Wasps you can basically neutralize, at least briefly, 8 targets.

Rush your fleet in and support your Wasps with Force Fields from Trojans or some ability from the Ulysses I as well as repair by Trilobites. By the time the EMP on the buildings wear off you should be in position to area EMP again with a Trojan or your own Triton.

If you have a Dreadnought, you should be able to wipe out the Capital Hangar quickly with its main gun although that power is notoriously unreliable. If you can do without, swap your Dreadnoughts for Hydra or Tritons.

Once the Sector is secure, destroy the last Support Hangar. Since the Sector is clear, you should have plenty of time to finish the final time-limited mission objective without interference. After that, the mission is basically won.

In this video you can see the reinforcements that enter Sector 2 once you have opened the gate from Sector 1 to Sector 2. A lot easier to handle if you already controlled the Stations around the gate.